Mercurial > repos > galaxyp > openms_siriusadapter

comparison SiriusAdapter.xml @ 6:ac6f09817679 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:11:33 +0000
parents 01731de4b735
children 2d655933d65f
comparison
equal deleted inserted replaced
5:1a6f39227aca 6:ac6f09817679
73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
74 && mv '@EXECUTABLE@.ctd' '$ctd_out' 74 && mv '@EXECUTABLE@.ctd' '$ctd_out'
75 #end if]]></command> 75 #end if]]></command>
76 <configfiles> 76 <configfiles>
77 <inputs name="args_json" data_style="paths"/> 77 <inputs name="args_json" data_style="paths"/>
78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
79 </configfiles> 79 </configfiles>
80 <inputs> 80 <inputs>
81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> 81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/> 82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
83 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help=""> 83 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
137 <expand macro="list_string_san"/> 137 <expand macro="list_string_san"/>
138 </param> 138 </param>
139 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/> 139 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
140 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/> 140 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
141 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/> 141 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
142 <param name="cores" argument="-sirius:cores" type="integer" optional="true" min="1" value="1" label="The number of cores SIRIUS is allowed to use on the system" help=""/>
143 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/> 142 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
144 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/> 143 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
145 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/> 144 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
146 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/> 145 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
147 </section> 146 </section>
148 <expand macro="adv_opts_macro"> 147 <expand macro="adv_opts_macro">
149 <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/> 148 <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/>
150 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 149 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
151 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 150 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
152 <expand macro="list_string_san"/> 151 <expand macro="list_string_san"/>
153 </param> 152 </param>
154 </expand> 153 </expand>
155 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 154 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
156 <option value="out_sirius_FLAG">out_sirius (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option> 155 <option value="out_sirius_FLAG">out_sirius (MzTab Output file for SiriusAdapter results)</option>
157 <option value="out_fingerid_FLAG">out_fingerid (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option> 156 <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
158 <option value="out_ms_FLAG">out_ms (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option> 157 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
159 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 158 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
160 </param> 159 </param>
161 </inputs> 160 </inputs>
162 <outputs> 161 <outputs>
163 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab"> 162 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab">
181 <expand macro="manutest_SiriusAdapter"/> 180 <expand macro="manutest_SiriusAdapter"/>
182 </tests> 181 </tests>
183 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry 182 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
184 183
185 184
186 For more information, visit http://www.openms.de/documentation/UTILS_SiriusAdapter.html]]></help> 185 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SiriusAdapter.html]]></help>
187 <expand macro="references"/> 186 <expand macro="references"/>
188 </tool> 187 </tool>